The gene function prediction challenge: Large language models and knowledge graphs to the rescue DOI

Rohan Shawn Sunil,

Shan Chun Lim,

Manoj Itharajula

et al.

Current Opinion in Plant Biology, Journal Year: 2024, Volume and Issue: 82, P. 102665 - 102665

Published: Nov. 22, 2024

Language: Английский

Exploring Pan-Genomes: An Overview of Resources and Tools for Unraveling Structure, Function, and Evolution of Crop Genes and Genomes DOI Creative Commons
Sushma Naithani, Cecilia Deng, Sunil Kumar Sahu

et al.

Biomolecules, Journal Year: 2023, Volume and Issue: 13(9), P. 1403 - 1403

Published: Sept. 17, 2023

The availability of multiple sequenced genomes from a single species made it possible to explore intra- and inter-specific genomic comparisons at higher resolution build clade-specific pan-genomes several crops. crops constructed various cultivars, accessions, landraces, wild ancestral represent compendium genes structural variations allow researchers search for the novel alleles that were inadvertently lost in domesticated during historical process crop domestication or extensive plant breeding. Fortunately, many valuable associated with desirable traits like disease resistance, abiotic stress tolerance, architecture, nutrition qualities exist species, relatives. ancestors landraces can be introduced back high-yielding varieties modern by implementing classical breeding, selection, transgenic/gene editing approaches. Thus, pan-genomic represents great leap research offers new avenues targeted breeding mitigate impact global climate change. Here, we summarize tools used pan-genome assembly annotations, web-portals hosting pan-genomes, etc. Furthermore, highlight few discoveries using approach future potential this emerging field study.

Language: Английский

Citations

12
Detecting novel plant pathogen threats to food system security by integrating the Plant Reactome and remote sensing DOI
Seth C. Murray, Aart Verhoef, Alper Adak

et al.

Current Opinion in Plant Biology, Journal Year: 2025, Volume and Issue: 83, P. 102684 - 102684

Published: Jan. 5, 2025

Language: Английский

Citations

0
Genome-wide association study to identify candidate genes for submergence tolerance during rice seed germination DOI
Qiuyu Zhang, Bing Han, Di Cui

et al.

Theoretical and Applied Genetics, Journal Year: 2025, Volume and Issue: 138(2)

Published: Feb. 1, 2025

Language: Английский

Citations

0
Deep Neural Network‐Mining of Rice Drought‐Responsive TF‐TAG Modules by a Combinatorial Analysis of ATAC‐Seq and RNA‐Seq DOI
Jingpeng Liu,

Ximiao Shi,

Zhitai Zhang

et al.

Plant Cell & Environment, Journal Year: 2025, Volume and Issue: unknown

Published: March 31, 2025

ABSTRACT Drought is a critical risk factor that impacts rice growth and yields. Previous studies have focused on the regulatory roles of individual transcription factors in response to drought stress. However, there limited understanding multi‐factor stresses gene networks their mechanisms action. In this study, we utilised data from JASPAR database compile comprehensive dataset binding sites rice, Arabidopsis, barley genomes. We employed PyTorch framework for machine learning develop nine‐layer convolutional deep neural network TFBind. Subsequently, obtained RNA‐seq ATAC‐seq related abiotic stress public database. Utilising integrative analysis WGCNA ATAC‐seq, effectively identified associated with open chromatin regions drought. Interestingly, only 81% directly bound opened genes by testing TFBind model. By approach 15 drought‐responsive corresponding targets, which enriched terms protein transport, allocation, nitrogen compound transport. This provides valuable tool predicting TF‐TAG‐opened modules during biological processes.

Language: Английский

Citations

0
Exploring Pan-Genomes of Crops: Genomic Resources and Tools for Unraveling Gene Evolution, Function, and Adaptation DOI Open Access
Sushma Naithani, Cecilia Deng, Sunil Kumar Sahu

et al.

Published: Aug. 23, 2023

The availability of multiple sequenced genomes from a single species made it possible to explore intra- and inter-specific genomic comparisons at higher resolution build clade-specific pangenomes several crops. pan-genomes crops constructed various cultivars/accessions, landraces, wild ancestral represent compendium genes structural variations allow researchers search for the novel alleles that were inadvertently lost in domesticated during historical process crop domestication or extensive plant breeding. Fortunately, many valuable associated with desirable traits like disease resistance, abiotic stress tolerance, architecture, nutrition qualities exist species, relatives. novels ancestors landraces can be introduced back high-yielding varieties modern by implementing classical breeding, selection, transgenic/gene editing approaches. Thus, pan-genomic represents great leap research offers new avenues targeted breeding mitigating impact global climate change. Here we summarize tools used pangenome assembly annotations, web-portals hosting pangenomes. Furthermore, highlight few discoveries using approach its future potential.

Language: Английский

Citations

5
Plant Reactome Knowledgebase: empowering plant pathway exploration and OMICS data analysis DOI Creative Commons
Parul Gupta, Justin Elser,

Elizabeth Hooks

et al.

Nucleic Acids Research, Journal Year: 2023, Volume and Issue: 52(D1), P. D1538 - D1547

Published: Nov. 20, 2023

Plant Reactome (https://plantreactome.gramene.org) is a freely accessible, comprehensive plant pathway knowledgebase. It provides curated reference pathways from rice (Oryza sativa) and gene-orthology-based projections to 129 additional species, spanning single-cell photoautotrophs, non-vascular plants, higher thus encompassing wide-ranging taxonomic diversity. Currently, houses collection of 339 pathways, covering metabolic transport hormone signaling, genetic regulations developmental processes, intricate transcriptional networks that orchestrate plant's response abiotic biotic stimuli. Beyond being mere repository, serves as dynamic data discovery platform. Users can analyze visualize omics data, such gene expression, gene-gene interaction, proteome, metabolome all within the rich context pathways. dedicated fostering interoperability, upholding global standards, embracing tenets Findable, Accessible, Interoperable Re-usable (FAIR) policy.

Language: Английский

Citations

4
Investigation on the Potential Functions of ZmEPF/EPFL Family Members in Response to Abiotic Stress in Maize DOI Open Access
Rui Liu, Keli Xu, Yu Li

et al.

International Journal of Molecular Sciences, Journal Year: 2024, Volume and Issue: 25(13), P. 7196 - 7196

Published: June 29, 2024

Maize is an important crop used for food, feed, and fuel. Abiotic stress factor affecting maize yield. The EPF/EPFL gene family encodes class-specific secretory proteins that play role in the response to abiotic plants. In order explore utilize maize, members were systematically identified, their chromosomal localization, physicochemical properties, cis-acting element prediction promoters, phylogenetic tree construction, expression pattern analysis carried out using bioinformatics techniques. A total of 18 ZmEPF/EPFL identified which are mostly alkaline a small portion acidic. Subcellular localization results showed ZmEPF6, ZmEPF12, ZmEPFL2 localized nucleus cytoplasm. Analysis elements revealed contain regulatory such as light response, anoxic, low temperature, hormone elements. RT-qPCR these indeed responding cold treatments. These this study provide theoretical basis improving resistance future research.

Language: Английский

Citations

1
Molecular mechanism of abiotic stress regulation in crop plants DOI

D Akash,

Dey Avishek

Elsevier eBooks, Journal Year: 2024, Volume and Issue: unknown, P. 23 - 39

Published: Jan. 1, 2024

Language: Английский

Citations

0
Disruption of the OsWRKY71 transcription factor gene results in early rice seed germination under normal and cold stress conditions DOI Creative Commons
Santiago Bataller, James Davis, Lingkun Gu

et al.

BMC Plant Biology, Journal Year: 2024, Volume and Issue: 24(1)

Published: Nov. 18, 2024

Abstract Background Early seed germination in crops can confer a competitive advantage against weeds and reduce the time to maturation harvest. WRKY transcription factors regulate many aspects of plant development including dormancy germination. Both positive negative regulators have been reported plants such as rice Arabidopsis. Using transient expression system, we previously demonstrated that OsWRKY71 is regulator gibberellin (GA) signaling aleurone cells likely forms “repressosome” complex with other transcriptional repressors. Hence, it has potential impact properties. Results In this study, demonstrate , Group IIa gene, appeared at same seed-bearing plants. Rice mutants lacking seeds embryos germinate earlier than wildtype controls. oswrky71 layers, α-amylase activity was hypersensitive stimulation by GA 3 hyposensitive inhibition abscisic acid (ABA). intact also ABA. Transcriptomic profiling during embryo early post-germination growth demonstrates influences 9–17% genes dry imbibing embryos. Compared embryos, mutant transcriptomes large temporal shifts 4, 8 12 h after imbibition (HAI). Importantly, involved ABA-dependent were downregulated oswrky71-1 . This displayed altered multiple ABA receptors ( OsPYLs/RCARs ) control VP1-SDR4-DOG1L branch promotes dormancy. Association studies reveal an -containing quantitative trait locus low-temperature germinability, qLTG-2 Indeed, germinated 15 °C. Conclusions Group-IIa factor master It most primary candidate germinability QTL, We propose knockouts generate varieties improved properties under normal or conditions.

Language: Английский

Citations

0
The gene function prediction challenge: Large language models and knowledge graphs to the rescue DOI

Rohan Shawn Sunil,

Shan Chun Lim,

Manoj Itharajula

et al.

Current Opinion in Plant Biology, Journal Year: 2024, Volume and Issue: 82, P. 102665 - 102665

Published: Nov. 22, 2024

Language: Английский

Citations

0